The GEIRA (Gene-Environment and Gene-Gene Interaction Research Application) algorithm and subsequent program is dedicated to genome-wide gene-environment and gene-gene interaction analysis. It implements concepts of both additive and multiplicative interaction as well as calculations based on dominant, recessive and co-dominant genetic models, respectively. Estimates of interactions are incorporated in a single table to make the output easily read. The algorithm is coded in both SAS and R. GEIRA is freely available to non-commercial users at http://www.epinet.se. Additional information, including user's manual and example datasets is available online at http://www.epinet.se.